Grid Cell and Non-Grid Cell Recordings from Layer II/III of Medial Entorhinal Cortex from 6 rats (1-7 sessions each) During Active Exploration and Overnight Sleep

GENERAL INFORMATION: 
Data are rat's positional data and recordings obtained from superficial layers of the medial entorhinal cortex (layer II/III). 
Data are for 6 rats, from 1-7 sessions each, in which each session contains two "tasks" across two days. 

The Open Field task required rats to randomly forage around a 100 x 100 cm arena for small cereal rewards. 
The Overnight task was simply a rat placed in a 60 x 60 cm box for overnight recordings, with food, water and 
enrichment items provided. 

The Open Field session was repeated the following morning (Day 2), and the units' firing analyzed, to confirm 
stability of recordings. Data from day 1 only was analyzed for the publication. Data from day 2 was used only 
to confirm stability of overnight recordings.

Each Open Field session included three 20-minute bouts of task performance, with 10 minutes
of rest before and after each bout. During 'rest,' rats were removed from the track/box and placed in an
elevated and towel lined flower pot. Data from these interwoven 10 minutes rest sessions are not provided here.

For additional details, please see the publication: 
Trettel, S.G., Trimper, J.B., Hwaun, E., Fiete, I.R., & Colgin, L.L. (2019). Grid cell co-activity patterns 
during sleep reflect spatial overlap of grid fields during active behaviors. Nature Neuroscience, 22(4), 609-617.
https://www.ncbi.nlm.nih.gov/pubmed/30911183



------------------------------------------------------
RAW DATA DIRECTORY ORGANIZATION: 
Within the main folder, each of the 6 rats has a subdirectory named according to the rat's ID. 

Within each rat's subdirectory, a subdirectory exists for each experimental session. 

Within each session's subdirectory, a subdirectory exists for each of two recording days. 
Also within this folder is a text file indicating the names of the unit cluster files, which 
are located within each bout subdirectory (to be described later) and contain the spike times 
for each unit. Names indicate tetrode and unit number (e.g., TT8_1.t = tetrode 8, unit 1). Non-grid cells 
are additionally tagged with '_NonGC.t' whereas confirmed grid cells do not include this tag. 

Within each Day 1 subdirectory, a subdirectory for each 'task' can be found. A text file is also
included noting the date at which that session was recorded. 

Within each 'task' subdirectory (i.e., OpenField, Overnight), a subdirectory exists for 
each bout of 'task performance.' I am employing '' here because the Overnight 'task' did not require any
particular behaviors of the rat. For OpenField data, these bouts are called 'Begin' and
for Overnight, these bout subdirectories are titled 'Sleep.' 

Data contained in Sleep subdirectories corresponds to times when two independent reviewers both agreed, 
based on viewing videos of the animals' behavior, that the rat was asleep rather than simply immobile. 
Thus, data is not provided for the entirety of the overnight recording session, but only when rats were asleep. 

Each bout directory contains the *.t files (unit spike times) and the *.nvt file (raw position data for 
each LED on the rat's headstage). Neuralynx functions can be used to read in this raw data. Functions 
available on the Colgin Lab GitHub page (e.g., Readtfile and read_in_coords) demonstrate how to employ
these Neuralynx functions. 

LFPs are not provided here as they are still being analyzed for a paper in preparation.

GitHub page: https://github.com/jtrimper/ColginLabCode



------------------------------------------------------
MATLAB DATA STRUCTURE ORGANIZATION: 

1) File name: 'Rat_Data_Struct_040819.mat'
2) Description: This data structure contains rat's positional data for open field bouts and spike-time information for each unit during open field and sleep bouts.
3) Highest level of organization: rat
4) Subfield structure: 
-rat
--name: string specifying rat's ID (e.g., Rat-20)
--session
----day
------task: 2 'tasks' (1 = Open Field; 2 = Overnight)
--------name
--------bout
----------coords: nx3 matrix, where (:,1) = time for each video frame, (:,2) = x position for each frame, and (:,3) = y position for each frame; [available only for OpenField session]
----------runTimes OR REMTimes OR nRemTimes: nx2 matrix indicating the start time (:,1) and stop time (:,2), in seconds, in which the rat was in each behavioral state. See publication for functional definition of each behavioral state. Available for day 1 only.
----------unit: data for each unit
------------ID: tetrode and cluster number
------------type: scalar indicating whether unit is a grid cell (1) or a non-grid cell (2)
------------spkTms: nx1 vector indicating time for each action potential, in seconds